Fluorine in PDB 7rdx: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class

Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class:
2.7.7.48; 3.6.4.12; 3.6.4.13;

Other elements in 7rdx:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms
Zinc (Zn) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class (pdb code 7rdx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class, PDB code: 7rdx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7rdx

Go back to Fluorine Binding Sites List in 7rdx
Fluorine binding site 1 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:115.0
occ:1.00
F1 E:AF3706 0.0 115.0 1.0
AL E:AF3706 1.8 115.0 1.0
MG E:MG705 2.0 108.5 1.0
O3B E:ADP704 2.2 115.4 1.0
HH12 E:ARG443 2.4 130.5 1.0
HH22 E:ARG443 2.7 130.5 1.0
O1A E:ADP704 2.8 115.4 1.0
NH1 E:ARG443 3.0 130.5 1.0
F2 E:AF3706 3.1 115.0 1.0
F3 E:AF3706 3.1 115.0 1.0
NH2 E:ARG443 3.2 130.5 1.0
PB E:ADP704 3.3 115.4 1.0
CZ E:ARG443 3.4 130.5 1.0
HA2 E:GLY538 3.4 123.4 1.0
O3A E:ADP704 3.5 115.4 1.0
HH11 E:ARG443 3.6 130.5 1.0
HH21 E:ARG567 3.6 133.8 1.0
OG E:SER289 3.6 104.9 1.0
PA E:ADP704 3.7 115.4 1.0
H E:GLY285 3.8 119.3 1.0
O E:GLY538 3.8 123.4 1.0
NH2 E:ARG567 3.8 133.8 1.0
O2B E:ADP704 3.8 115.4 1.0
HH21 E:ARG443 3.9 130.5 1.0
HH22 E:ARG567 4.0 133.8 1.0
HA2 E:GLY285 4.2 119.3 1.0
CA E:GLY538 4.2 123.4 1.0
C E:GLY538 4.3 123.4 1.0
H E:GLY538 4.3 123.4 1.0
CZ E:ARG567 4.4 133.8 1.0
HB2 E:SER289 4.4 104.9 1.0
HE E:ARG567 4.5 133.8 1.0
N E:GLY285 4.5 119.3 1.0
O1B E:ADP704 4.6 115.4 1.0
NE E:ARG443 4.6 130.5 1.0
CB E:SER289 4.6 104.9 1.0
NE E:ARG567 4.6 133.8 1.0
N E:GLY538 4.7 123.4 1.0
O2A E:ADP704 4.8 115.4 1.0
OE2 E:GLU375 4.8 96.7 1.0
O5' E:ADP704 4.8 115.4 1.0
CA E:GLY285 4.9 119.3 1.0
H E:SER289 4.9 104.9 1.0
HA3 E:GLY538 5.0 123.4 1.0
HE2 E:LYS288 5.0 103.1 1.0

Fluorine binding site 2 out of 6 in 7rdx

Go back to Fluorine Binding Sites List in 7rdx
Fluorine binding site 2 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:115.0
occ:1.00
F2 E:AF3706 0.0 115.0 1.0
AL E:AF3706 1.8 115.0 1.0
HE22 E:GLN404 2.2 113.5 1.0
O3B E:ADP704 2.8 115.4 1.0
NE2 E:GLN404 3.0 113.5 1.0
F1 E:AF3706 3.1 115.0 1.0
F3 E:AF3706 3.1 115.0 1.0
HA E:PRO284 3.2 119.0 1.0
HH22 E:ARG567 3.2 133.8 1.0
HZ1 E:LYS288 3.3 103.1 1.0
H E:GLY285 3.4 119.3 1.0
MG E:MG705 3.4 108.5 1.0
OE2 E:GLU375 3.5 96.7 1.0
OE1 E:GLN404 3.6 113.5 1.0
NH2 E:ARG567 3.6 133.8 1.0
HE21 E:GLN404 3.6 113.5 1.0
CD E:GLN404 3.7 113.5 1.0
HB3 E:PRO284 3.8 119.0 1.0
HH12 E:ARG567 3.8 133.8 1.0
HE2 E:LYS288 3.8 103.1 1.0
HE3 E:LYS288 4.0 103.1 1.0
HH21 E:ARG567 4.0 133.8 1.0
CA E:PRO284 4.0 119.0 1.0
NZ E:LYS288 4.0 103.1 1.0
N E:GLY285 4.1 119.3 1.0
CZ E:ARG567 4.2 133.8 1.0
CE E:LYS288 4.2 103.1 1.0
NH1 E:ARG567 4.2 133.8 1.0
PB E:ADP704 4.2 115.4 1.0
CB E:PRO284 4.2 119.0 1.0
HB2 E:PRO284 4.3 119.0 1.0
HZ2 E:LYS288 4.3 103.1 1.0
CD E:GLU375 4.4 96.7 1.0
OE1 E:GLU375 4.5 96.7 1.0
HA2 E:GLY538 4.5 123.4 1.0
HG2 E:GLN537 4.6 121.3 1.0
C E:PRO284 4.7 119.0 1.0
HZ3 E:LYS288 4.7 103.1 1.0
HH12 E:ARG443 4.7 130.5 1.0
H E:GLY538 4.8 123.4 1.0
O2B E:ADP704 4.8 115.4 1.0
HG3 E:GLN537 4.8 121.3 1.0
HH11 E:ARG567 4.8 133.8 1.0
O1B E:ADP704 4.9 115.4 1.0

Fluorine binding site 3 out of 6 in 7rdx

Go back to Fluorine Binding Sites List in 7rdx
Fluorine binding site 3 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:115.0
occ:1.00
F3 E:AF3706 0.0 115.0 1.0
AL E:AF3706 1.8 115.0 1.0
MG E:MG705 2.0 108.5 1.0
OE2 E:GLU375 2.1 96.7 1.0
OG E:SER289 2.6 104.9 1.0
F1 E:AF3706 3.1 115.0 1.0
F2 E:AF3706 3.1 115.0 1.0
HE2 E:LYS288 3.3 103.1 1.0
CD E:GLU375 3.3 96.7 1.0
O3B E:ADP704 3.4 115.4 1.0
O2B E:ADP704 3.6 115.4 1.0
HA2 E:GLY538 3.7 123.4 1.0
HG2 E:GLU375 3.8 96.7 1.0
HB2 E:LYS288 3.8 103.1 1.0
HE3 E:LYS288 3.9 103.1 1.0
CE E:LYS288 4.0 103.1 1.0
CG E:GLU375 4.0 96.7 1.0
H E:SER289 4.1 104.9 1.0
PB E:ADP704 4.1 115.4 1.0
CB E:SER289 4.1 104.9 1.0
OD1 E:ASP374 4.2 91.4 1.0
HG3 E:GLU375 4.2 96.7 1.0
OE1 E:GLU375 4.3 96.7 1.0
HB3 E:SER289 4.5 104.9 1.0
HZ1 E:LYS288 4.5 103.1 1.0
O1A E:ADP704 4.5 115.4 1.0
HB2 E:SER289 4.5 104.9 1.0
N E:SER289 4.5 104.9 1.0
CA E:GLY538 4.6 123.4 1.0
HE22 E:GLN404 4.7 113.5 1.0
CA E:SER289 4.8 104.9 1.0
CB E:LYS288 4.8 103.1 1.0
OD2 E:ASP374 4.8 91.4 1.0
HA E:SER289 4.8 104.9 1.0
NZ E:LYS288 4.9 103.1 1.0
HA3 E:GLY538 4.9 123.4 1.0
CG E:ASP374 5.0 91.4 1.0

Fluorine binding site 4 out of 6 in 7rdx

Go back to Fluorine Binding Sites List in 7rdx
Fluorine binding site 4 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:178.2
occ:1.00
F1 F:AF31005 0.0 178.2 1.0
AL F:AF31005 1.8 178.2 1.0
H F:GLY285 2.0 175.0 1.0
O3B F:ADP1003 2.2 177.4 1.0
N F:GLY285 2.8 175.0 1.0
F3 F:AF31005 3.1 178.2 1.0
F2 F:AF31005 3.1 178.2 1.0
HA F:PRO284 3.1 175.7 1.0
PB F:ADP1003 3.1 177.4 1.0
HA2 F:GLY285 3.2 175.0 1.0
O1B F:ADP1003 3.2 177.4 1.0
HH22 F:ARG443 3.3 176.7 1.0
CA F:GLY285 3.5 175.0 1.0
HH21 F:ARG443 3.6 176.7 1.0
C F:PRO284 3.7 175.7 1.0
NH2 F:ARG443 3.8 176.7 1.0
CA F:PRO284 3.8 175.7 1.0
H F:THR286 3.8 175.6 1.0
HH22 F:ARG567 3.8 175.7 1.0
HZ1 F:LYS288 3.9 173.3 1.0
HB3 F:PRO284 4.0 175.7 1.0
O2B F:ADP1003 4.0 177.4 1.0
HH21 F:ARG567 4.1 175.7 1.0
HA3 F:GLY285 4.2 175.0 1.0
NH2 F:ARG567 4.3 175.7 1.0
O3A F:ADP1003 4.4 177.4 1.0
CB F:PRO284 4.4 175.7 1.0
N F:THR286 4.5 175.6 1.0
O2A F:ADP1003 4.5 177.4 1.0
C F:GLY285 4.6 175.0 1.0
H F:GLY287 4.7 171.8 1.0
O5' F:ADP1003 4.8 177.4 1.0
NZ F:LYS288 4.8 173.3 1.0
HB2 F:PRO284 4.9 175.7 1.0
O F:PRO284 4.9 175.7 1.0
PA F:ADP1003 4.9 177.4 1.0
HE2 F:LYS288 4.9 173.3 1.0
O F:PRO283 4.9 175.8 1.0

Fluorine binding site 5 out of 6 in 7rdx

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Fluorine binding site 5 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:178.2
occ:1.00
F2 F:AF31005 0.0 178.2 1.0
H F:THR286 1.7 175.6 1.0
AL F:AF31005 1.8 178.2 1.0
HZ1 F:LYS288 2.0 173.3 1.0
N F:THR286 2.5 175.6 1.0
OG1 F:THR286 2.5 175.6 1.0
H F:GLY285 2.6 175.0 1.0
HZ3 F:LYS288 2.6 173.3 1.0
O1B F:ADP1003 2.6 177.4 1.0
H F:GLY287 2.6 171.8 1.0
NZ F:LYS288 2.7 173.3 1.0
N F:GLY285 3.0 175.0 1.0
O2B F:ADP1003 3.1 177.4 1.0
HG1 F:THR286 3.1 175.6 1.0
F3 F:AF31005 3.1 178.2 1.0
PB F:ADP1003 3.1 177.4 1.0
F1 F:AF31005 3.1 178.2 1.0
O F:PRO283 3.1 175.8 1.0
HZ2 F:LYS288 3.3 173.3 1.0
CA F:THR286 3.3 175.6 1.0
N F:GLY287 3.3 171.8 1.0
HE2 F:LYS288 3.4 173.3 1.0
C F:GLY285 3.4 175.0 1.0
CB F:THR286 3.4 175.6 1.0
HA F:PRO284 3.5 175.7 1.0
CA F:GLY285 3.5 175.0 1.0
HG3 F:LYS288 3.5 173.3 1.0
HA2 F:GLY285 3.6 175.0 1.0
CE F:LYS288 3.6 173.3 1.0
O3B F:ADP1003 3.6 177.4 1.0
C F:PRO284 3.8 175.7 1.0
H F:LYS288 3.8 173.3 1.0
HG23 F:THR286 3.8 175.6 1.0
C F:THR286 3.8 175.6 1.0
CA F:PRO284 4.1 175.7 1.0
CG2 F:THR286 4.1 175.6 1.0
C F:PRO283 4.2 175.8 1.0
HA F:THR286 4.2 175.6 1.0
HB F:THR286 4.2 175.6 1.0
HE3 F:LYS288 4.3 173.3 1.0
HG21 F:THR286 4.3 175.6 1.0
CG F:LYS288 4.4 173.3 1.0
HA3 F:GLY285 4.5 175.0 1.0
N F:LYS288 4.5 173.3 1.0
CA F:GLY287 4.5 171.8 1.0
O F:GLY285 4.6 175.0 1.0
H5'2 F:ADP1003 4.6 177.4 1.0
HA2 F:GLY287 4.6 171.8 1.0
N F:PRO284 4.6 175.7 1.0
CD F:LYS288 4.6 173.3 1.0
O3A F:ADP1003 4.6 177.4 1.0
O F:PRO284 4.7 175.7 1.0
HA3 F:GLY282 4.7 174.9 1.0
O F:GLY282 4.8 174.9 1.0
C F:GLY282 4.9 174.9 1.0
HG22 F:THR286 5.0 175.6 1.0
HG2 F:LYS288 5.0 173.3 1.0

Fluorine binding site 6 out of 6 in 7rdx

Go back to Fluorine Binding Sites List in 7rdx
Fluorine binding site 6 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:178.2
occ:1.00
F3 F:AF31005 0.0 178.2 1.0
AL F:AF31005 1.8 178.2 1.0
HZ1 F:LYS288 2.0 173.3 1.0
NZ F:LYS288 2.6 173.3 1.0
HA F:PRO284 2.7 175.7 1.0
HZ2 F:LYS288 2.7 173.3 1.0
HE3 F:LYS288 2.9 173.3 1.0
HE2 F:LYS288 3.0 173.3 1.0
CE F:LYS288 3.1 173.3 1.0
F2 F:AF31005 3.1 178.2 1.0
F1 F:AF31005 3.1 178.2 1.0
HE21 F:GLN404 3.2 172.5 1.0
HZ3 F:LYS288 3.4 173.3 1.0
H F:GLY285 3.6 175.0 1.0
CA F:PRO284 3.6 175.7 1.0
NE2 F:GLN404 3.8 172.5 1.0
O F:GLY282 4.0 174.9 1.0
O F:PRO283 4.0 175.8 1.0
HE22 F:GLN404 4.1 172.5 1.0
HG3 F:GLN404 4.1 172.5 1.0
N F:PRO284 4.2 175.7 1.0
O3B F:ADP1003 4.2 177.4 1.0
N F:GLY285 4.2 175.0 1.0
HB3 F:PRO284 4.3 175.7 1.0
C F:PRO283 4.3 175.8 1.0
HG3 F:GLN537 4.3 171.5 1.0
C F:PRO284 4.5 175.7 1.0
CB F:PRO284 4.5 175.7 1.0
O2B F:ADP1003 4.5 177.4 1.0
CD F:LYS288 4.6 173.3 1.0
HG3 F:PRO284 4.6 175.7 1.0
HE21 F:GLN537 4.6 171.5 1.0
HB2 F:ASP401 4.7 173.0 1.0
CD F:GLN404 4.7 172.5 1.0
PB F:ADP1003 4.7 177.4 1.0
H F:THR286 4.7 175.6 1.0
OE2 F:GLU375 4.7 171.8 1.0
CG F:GLN404 4.8 172.5 1.0
HG3 F:LYS288 4.9 173.3 1.0
HD3 F:LYS288 4.9 173.3 1.0
C F:GLY282 4.9 174.9 1.0
OG1 F:THR286 5.0 175.6 1.0
CG F:PRO284 5.0 175.7 1.0
O1B F:ADP1003 5.0 177.4 1.0

Reference:

J.Chen, Q.Wang, B.Malone, E.C.Llewellyn, K.Maruthi, E.T.Eng, J.Perry, E.A.Campbell, D.E.Shaw, S.A.Darst. Ensemble Cryo-Electron Microscopy Reveals Conformational States of the Sars-Cov-2 Helicase Replication-Transcription Complex Biorxiv 2021.
DOI: 10.1101/2021.11.10.468168
Page generated: Thu Nov 25 09:15:29 2021

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